Response of Rhizobacterial Community to Biochar Amendment in Coal Mining Soils with Brachiaria Decumbens as Pioneer Plant

References

• Beesley, L., E. Moreno-Jiménez, J. L. Gomez-Eyles, E. Harris, B. Robinson, and T. Sizmur. 2011. A review of biochars’ potential role in the remediation, revegetation and restoration of contaminated soils. Environ. Pollut. 159 (12):3269–82. doi:10.1016/j.envpol.2011.07.023.
   PubMed Web of Science ®Google Scholar
• Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30 (15):2114–20. doi:10.1093/bioinformatics/btu170.
   PubMed Web of Science ®Google Scholar
• Caporaso, J. G., J. Kuczynski, J. Stombaugh, K. Bittinger, F. D. Bushman, E. K. Costello, N. Fierer, A. Gonzalez Peña, J. K. Goodrich, J. Gordon, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat. Methods. 7 (5):335–36. doi:10.1038/nmeth.f.303.
   PubMed Web of Science ®Google Scholar
• Chen, J., X. Liu, J. Zheng, B. Zhang, H. Lu, Z. Chi, G. Pan, L. Li, J. Zheng, X. Zhang, et al. 2013. Biochar soil amendment increased bacterial but decreased fungal gene abundance with shifts in community structure in a slightly acid rice paddy from Southwest China. Appl. Soil. Ecol. 71:33–44. doi:10.1016/j.apsoil.2013.05.003.
   Web of Science ®Google Scholar
• Dai, J., H. Wu, C. Zhang, G. Zeng, J. Liang, S. Guo, X. Li, L. Huang, L. Lu, and Y. Yuan. 2016. Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China. J. Biosci. Bioeng. 122 (3):345–50. doi:10.1016/j.jbiosc.2016.01.016.
   PubMed Web of Science ®Google Scholar
• De Tender, C. A., J. Debode, B. Vandecasteele, T. D’Hose, P. Cremelie, A. Haegeman, T. Ruttink, P. Dawyndt, and M. Maes. 2016. Biological, physicochemical and plant health responses in lettuce and strawberry in soil or peat amended with biochar. Agric. Ecosyst. Environ. Appl. Soil Ecol. 107:1–12. doi:10.1016/j.apsoil.2016.05.001.
   Web of Science ®Google Scholar
• Edgar, R. C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26 (19):2460–61. doi:10.1093/bioinformatics/btq461.
   PubMed Web of Science ®Google Scholar
• Fellet, G., L. Marchiol, G. Delle Vedove, and A. Peressotti. 2011. Application of biochar on mine tailings: Effects and perspectives for land reclamation. Chemosphere 83 (9):1262–67. doi:10.1016/j.chemosphere.2011.03.053.
   PubMed Web of Science ®Google Scholar
• Gower, J. C. 2014. Principal Coordinates Analysis. In Wiley StatsRef: Statistics Reference Online, ed. N. Balakrishnan, T. Colton, B. Everitt, W. Piegorsch, F. Ruggeri and J. L. Teugels. New York: John Wiley and Sons Ltd. doi:10.1002/9781118445112.stat05670.
   Google Scholar
• Graber, E. R., L. Tsechansky, B. Lew, and E. Cohen. 2014. Reducing capacity of water extracts of biochars and their solubilization of soil Mn and Fe. Eur. J. Soil. Sci. 65 (1):162–72. doi:10.1111/ejss.12071.
   Web of Science ®Google Scholar
• Grifoni, A., M. Bazzicalupo, C. Di Serio, S. Fancelli, and R. Fani. 1995. Identification of Azospirillum strains by restriction fragment length polymorphism of the 16S rDNA and of the histidine operon. FEMS Microbiol. Lett. 127 (1–2):85–91. doi:10.1111/j.1574-6968.1995.tb07454.x.
   PubMed Web of Science ®Google Scholar
• Harter, J., P. Weigold, M. El-hadidi, D. H. Huson, A. Kappler, and S. Behrens. 2016. Soil biochar amendment shapes the composition of N2O-reducing microbial communities. Sci. Total Environ. 562:379–90. doi:10.1016/j.scitotenv.2016.03.220.
   PubMed Web of Science ®Google Scholar
• Jones, D. L., J. Rousk, G. Edwards-Jones, T. H. DeLuca, and D. V. Murphy. 2012. Biochar-mediated changes in soil quality and plant growth in a three year field trial. Soil Biol. Biochem. 45:113–24. doi:10.1016/j.soilbio.2011.10.012.
   Web of Science ®Google Scholar
• Khodadad, C. L. M., A. R. Zimmerman, S. J. Green, S. Uthandi, and J. S. Foster. 2011. Taxa-specific changes in soil microbial community composition induced by pyrogenic carbon amendments. Soil Biol. Biochem. 43 (2):385–92. doi:10.1016/j.soilbio.2010.11.005.
   Web of Science ®Google Scholar
• Kielak, A. M., C. C. Barreto, G. A. Kowalchuk, J. A. van Veen, and E. E. Kuramae. 2016. The Ecology of Acidobacteria: Moving beyong Genes and Genomas. Front Microbiol. 7:1–16. doi:10.3389/fmicb.2016.00744.
   PubMed Web of Science ®Google Scholar
• Kolton, M., Y. Meller Harel, Z. Pasternak, E. R. Graber, Y. Elad, and E. Cytryn. 2011. Impact of biochar application to soil on the root-associated bacterial community structure of fully developed greenhouse pepper plants. Appl. Environ. Microbiol. 77 (14):4924–30. doi:10.1128/AEM.00148-11.
   PubMed Web of Science ®Google Scholar
• Lehmann, J., J. Gaunt, and M. Rondon. 2006. Biochar sequestration in terrestrial ecosystems - A review. Mitig. Adapt. Strat. Glob. Change 11 (2):403–27. doi:10.1007/s11027-005-9006-5.
   Google Scholar
• Lehmann, J., M. C. Rillig, J. Thies, C. A. Masiello, W. C. Hockaday, and D. Crowley. 2011. Biochar effects on soil biota – A review. Soil Biol. Biochem. 43 (9):1812–36. doi:10.1016/j.soilbio.2011.04.022.
   Web of Science ®Google Scholar
• Liao, N., Q. Li, W. Zhang, G. Zhou, L. Ma, W. Min, J. Ye, and Z. Hou. 2016. Effects of biochar on soil microbial community composition and activity in drip-irrigated desert soil. Eur. J. Soil Biol. 72:27–34. doi:10.1016/j.ejsobi.2015.12.008.
   Web of Science ®Google Scholar
• Liu, C., N. Ding, Q. Fu, P. C. Brookes, J. Xu, B. Guo, Y. Lin, H. Li, and N. Li. 2016. The influence of soil properties on the size and structure of bacterial and fungal communities along a paddy soil chronosequence. Eur. J. Soil. Sci. 76:9–18.
   Google Scholar
• Lozupone, C., M. Hamady, and R. Knight. 2006. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7:371. doi:10.1186/1471-2105-7-371.
   PubMed Web of Science ®Google Scholar
• Lozupone, C., and R. Knight. 2005. UniFrac : A New Phylogenetic Method for Comparing Microbial Communities. Appl. Environ. Microbiol. 71 (12):8228–35. doi:10.1128/AEM.71.12.8228-8235.2005.
   PubMed Web of Science ®Google Scholar
• McMurdie, P. J., and S. Holmes. 2013. Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE 8:1–11. doi:10.1371/journal.pone.0061217.
   Web of Science ®Google Scholar
• Muyzer, G., E. C. de Waal, and A. G. Uitterlinden. 1993. Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl. Environ. Microbiol. 59 (3):695–700.
   PubMed Web of Science ®Google Scholar
• O’Neill, B., J. Grossman, M. T. Tsai, J. E. Gomes, J. Lehmann, J. Peterson, E. Neves, and J. E. Thies. 2009. Bacterial Community Composition in Brazilian Anthrosols and Adjacent Soils Characterized Using Culturing and Molecular Identification. Microb. Ecol. 58 (1):23–35. doi:10.1007/s00248-009-9515-y.
   PubMed Web of Science ®Google Scholar
• Rodríguez-Vila, A., E. F. Covelo, R. Forján, and V. Asensio. 2014. Phytoremediating a copper mine soil with Brassica juncea L., compost and biochar. Environ Sci Pollut Res Int 21 (19):11293–304. doi:10.1007/s11356-014-2993-6.
   PubMed Web of Science ®Google Scholar
• Steinbeiss, S., G. Gleixner, and M. Antonietti. 2009. Effect of biochar amendment on soil carbon balance and soil microbial activity. Soil Biol. Biochem. 41 (6):1301–10. doi:10.1016/j.soilbio.2009.03.016.
   Web of Science ®Google Scholar
• Sun, D., J. Meng, H. Liang, E. Yang, Y. Huang, W. Chen, L. Jiang, Y. Lan, W. Zhang, and J. Gao. 2015. Effect of volatile organic compounds absorbed to fresh biochar on survival of Bacillus Mucilaginosus and structure of soil microbial communities. J. Soils Sediments 15 (2):271–81. doi:10.1007/s11368-014-0996-z.
   Web of Science ®Google Scholar
• Sun, D., J. Meng, E. G. Xu, and W. Chen. 2016. Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months. Agric. Ecosyst. Environ. Appl. Soil Ecol. 100:135–43. doi:10.1016/j.apsoil.2015.12.012.
   Google Scholar
• Ussiri, D. A. N., P. A. Jacinthe, and R. Lal. 2014. Methods for determination of coal carbon in reclaimed minesoils: A review. Geoderma 214–215:155–67. doi:10.1016/j.geoderma.2013.09.015.
   Web of Science ®Google Scholar
• Valverde, J. R., S. Marín, and R. P. Mellado. 2014. Effect of Herbicide Combinations on Bt-Maize Rhizobacterial Diversity. J. Microbiol. Biotechnol. 24 (11):1473–83. doi:10.4014/jmb.1405.05054.
   PubMed Web of Science ®Google Scholar
• Wang, R., S. Wei, P. Jia, T. Liu, D. Hou, R. Xie, Z. Lin, J. Ge, Y. Qiao, X. Chang, et al. 2019. Biochar significantly alters rhizobacterial communities and reduces Cd concentration in rice grains grown on Cd-contaminated soils. Sci. Total Environ. 676:627–38. doi:10.1016/j.scitotenv.2019.04.133.
   PubMed Web of Science ®Google Scholar
• Whiteley, A. S., S. Jenkins, I. Waite, N. Kresoje, H. Payne, B. Mullan, R. Allcock, and A. O’Donnell. 2012. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J. Microbiol. Methods 91 (1):80–88. doi:10.1016/j.mimet.2012.09.017.
   PubMed Web of Science ®Google Scholar
• Xiao, W., Z. Hu, and Y. Fu. 2014. Zoning of land reclamation in coal mining area and new progresses for the past 10 years. Int. J. Coal Sci. Technol. 1 (2):177–83. doi:10.1007/s40789-014-0024-3.
   Google Scholar
• Xu, G., Y. Lv, J. Sun, H. Shao, and L. Wei. 2012. Recent Advances in Biochar Applications in Agricultural Soils: Benefits and Environmental Implications. Clean. 40:1093–98. doi:10.1002/clen.201100738.
   Google Scholar
• Xu, N., G. Tan, H. Wang, and X. Gai. 2016. Effect of biochar additions to soil on nitrogen leaching, microbial biomass and bacterial community structure. Eur. J. Soil Sci. 74:1–8.
   Google Scholar
• Yao, Q., J. Liu, Z. Yu, Y. Li, J. Jin, X. Liu, and G. Wang. 2017. Changes of bacterial community compositions after three years of biochar application in a black soil of northeast China. Agric. Ecosyst. Environ. Appl. Soil Ecol. 113:11–21. doi:10.1016/j.apsoil.2017.01.007.
   Web of Science ®Google Scholar
• Zeng, Q., D. Yanghong, and A. Shaoshan. 2016. Bacterial Community Responses to Soils along a Latitudinal and Vegetation Gradient on the Loess Plateau, China. PLoS ONE 11 (4):e0152894. doi:10.1371/journal.pone.0152894.
   PubMed Web of Science ®Google Scholar
• Zhang, M., M. Riaz, Z. Lin, X. Hao, C. Ming, and J. Cuncang. 2019. Investigating the effect of biochar and fertilizer on the composition and function of bacteria in red soil. Agric. Ecosyst. Environ. Appl. Soil Ecol. 139:107–16. doi:10.1016/j.apsoil.2019.03.021.
   Google Scholar
• Zheng, J., J. Chen, G. Pan, X. Liu, X. Zhang, L. Li, R. Bian, K. Chen, and J. Zheng. 2016. Biochar decreased microbial metabolic quotient and shifted community composition four years after a single incorporation in a slightly acid rice paddy from southwest China. Sci. Total Environ. 571:206–17. doi:10.1016/j.scitotenv.2016.07.135.
   PubMed Web of Science ®Google Scholar
• Zhu, X., B. Chen, L. Zhu, and B. Xing. 2017. Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review. Environ. Pollut. 227:98–115. doi:10.1016/j.envpol.2017.04.032.
   PubMed Web of Science ®Google Scholar